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A nice summary article about the benefits and risks of coffee consumption. Summary of effects of drinking coffee1) May potentially increase blood pressure, but also may lower the risk for coronary disease, and protect against heart disease. 2) May cut stroke risk by as much as 25%, 3) Linked to  improved glucose metabolism, reduced risk for type 2 diabetes, and promotion of weight loss in overweight patients. 4) May reduce the risk for several cancers. 5) Appears to slow the progression of dementia and Parkinson's disease. 6) A significantly decreased risk of developing depression. 7) Slows progression in alcoholic cirrhosis, hepatitis C, and NAFLD (non-alcoholic fatty liver disease). 8) May be beneficial in dry-eye syndrome, gout, and in preventing MRSA infection. 9) May increase blood pressure, anxiety, insomnia, tremor, withdrawal symptoms, and potential increased risk of glaucoma. From Medscape:

How Healthy Is Coffee? The Latest Evidence

Earlier this year, the Dietary Guidelines Advisory Committee (DGAC) released a report[1] stating that up to five cups of coffee per day, or up to 400 mg of caffeine, is not associated with long-term health risks. Not only that, they highlighted observational evidence that coffee consumption is associated with reduced risk for several diseases, including type 2 diabetes, cardiovascular disease (CVD), and neurodegenerative disorders. The body of data suggesting that moderate coffee—and, in all likelihood, tea—consumption is not only safe but beneficial in a variety of mental and medical conditions is growing fast.

A 2012 study of over 400,000 people, published in the New England Journal of Medicine, reported that coffee consumption is associated with a 10% reduction in all-cause mortality at 13-year follow-up.... It's important to note that much of the evidence on the potential health effects of coffee, caffeine, and other foods and nutrients is associational and doesn't prove causality—observational investigations come with limitations and often rely on error-prone methods such as patient questionnaires. However, the sheer volume of existing observational data linking coffee and/or caffeine with various health benefits—as well as, in many cases, evidence of a dose response—suggests that the most widely consumed stimulant in the world has positive influences on our health. 

Cardiovascular Disease:...However, when caffeine is ingested via coffee, enduring blood pressure elevations are small and cardiovascular risks may be balanced by protective properties. Coffee beans contain antioxidant compounds that reduce oxidation of low-density lipoprotein (LDL) cholesterol, and coffee consumption has been associated with reduced concentrations of inflammatory markers. Moderate coffee intake is associated with a lower risk for coronary heart disease as far out as 10 years, and data suggest that an average of two cups per day protects against heart failure.

Cerebrovascular Disease and Stroke: The vascular benefits of coffee are not lost on the brain. According to a 2011 meta-analysis, consuming between one and six cups per day reportedly cut stroke risk by 17%. A 22%-25% risk reduction was seen in a large sample of Swedish women followed for an average of 10 years.

Diabetes:...Numerous studies have linked regular coffee drinking with improved glucose metabolism, insulin secretion, and a significantly reduced risk for diabetes. Most recently, findings from a long-term study published this year suggest that coffee drinkers are roughly half as likely to develop type 2 diabetes as are nonconsumers, even after accounting for smoking, high blood pressure, and family history of diabetes.

Cancer: ...Evidence suggests that moderate to heavy coffee consumption can reduce the risk for numerous cancers, including endometrial (> 4 cups/day), prostate (6 cups/day), head and neck (4 cups/day), basal cell carcinoma (> 3 cups/day), melanoma,and breast cancer (> 5 cups/day). The benefits are thought to be at least partially due to coffee's antioxidant and antimutagenic properties.

Neurodegeneration: Beyond the short-term mental boost it provides, coffee also appears to benefit longer-term cognitive well-being. A 2012 study reported that patients with mild cognitive impairment and plasma caffeine levels of > 1200 ng/mL—courtesy of approximately three to five cups of coffee per day—avoided progression to dementia over the following 2-4 years. On a related note, a study from last year reported that caffeine consumption appears to enhance memory consolidation....Caffeinated coffee has long been thought to be neuroprotective in Parkinson disease (PD)....—as well as in multiple sclerosis

Depression: A 2011 study suggests that a boost in coffee consumption might also benefit our mental health: Women who drank two to three cups of coffee per day had a 15% decreased risk for depression compared with those who drank less than one cup per week. A 20% decreased risk was seen in those who drank four cups or more per day. Newer work also suggests that regular coffee drinking may be protective against depression.

Liver Disease: The liver might help break down coffee, but coffee might protect the liver (in some cases). Evidence suggests that coffee consumption slows disease progression in patients with alcoholic cirrhosis and hepatitis C, and reduces the risk of developing hepatocellular carcinoma. A 2012 study reported that coffee intake is associated with a lower risk for nonalcoholic fatty liver disease (NAFLD), while work published in 2014 found that coffee protects against liver fibrosis in those with already established NAFLD.

And That's Not All…: An assortment of other research suggests that coffee intake might also relieve dry-eye syndrome by increasing tear production, reduce the risk for gout, and potentially fight infection. Coffee and hot tea consumption were found to be protective against one of the medical community's most concerning bugs, methicillin-resistant Staphylococcus aureus (MRSA). While it remains unclear whether the beverages have systemic antimicrobial activity, study participants who reported any consumption of either were approximately half as likely to have MRSA in their nasal passages.

And Finally, the Risks: As is often the case, with benefits come risks, and coffee consumption certainly has negative medical and psychiatric effects to consider. Besides the aforementioned potential increase in blood pressure, coffee can incite or worsen anxiety, insomnia, and tremor and potentially elevate glaucoma risk. Also, given the potential severity of symptoms, caffeine withdrawal syndrome is included as a diagnosis in the DSM-5.

Much discussion about the link between gut bacteria and liver cancer, as well as the link between inflammation and cancer. Gut microbiome imbalances can cause health harms.

Bottom line: Try to improve your gut microbiome by eating a diet rich in fruits, vegetables, seeds, nuts, legumes, and whole grains.

From the Dec.4, 2014 issue of Nature: Microbiome: The bacterial tightrope

Imbalances in gut bacteria have been implicated in the progression from liver disease to cancer. The team's research, published last year, suggests that gut bacteria — which are part of the microbiome of bacteria and other microorganisms that live in and on the body — can play a crucial part in liver-cancer progression.

There are trillions of microorganisms in the human microbiome — they outnumber their host's cells by around ten to one — and their exact role in health and disease is only now starting to be explored. Studies have found that people with non-alcoholic fatty liver disease have a different composition of bacteria in their gut from healthy individuals2, 3

 Instead, she sees an emerging picture of liver disease and cancer as a process in which various factors — including a high-fat diet, alcoholism, genetic susceptibility and the microbiome — can each contribute to the progression from minor to severe liver damage, and from severe liver damage to cancer.

Flavell's research suggests that the liver has an important role in immune surveillance and helps to maintain bacterial balance in the gut. Specialized cells in the liver and intestines monitor the microbiome by keeping tabs on bacterial by-products as they pass through. These cells can detect infections and help to fight them.

But they can also pick up on subtler changes in the bacterial populations in the gut. When certain types of bacteria become too numerous — a state called dysbiosis — the immune system becomes activated and triggers inflammation, although at a lower level than it would for an infection... Now, research is emerging that suggests that dysbiosis and the immune reaction it provokes can even contribute to cancer.

He thinks that at least part of this mechanism involves disruption in the balance of the various species of bacteria in the gut. An out-of-balance microbiome promotes a constant state of inflammation, which can contribute to cancer progression, Schwabe says. This aligns with the picture that is emerging of cancer, in general, as an inflammatory process: the same immune reactions that help the body to fight infection and disease can also promote unchecked cell growth.

Some of the earliest research on the human microbiome, published in 2006, demonstrated that the balance of gut bacteria in obese people is different from that in people of healthy weight. In particular, obese people tend to have greater numbers of the bacteria that produce DCA (deoxycholic acid) and other secondary bile acids.

This line of research points to the microbiome as one potential link between obesity and liver-cancer risk . And, much like Schwabe's work, Hara's results indicate that several factors converge to promote cancer: in this case, bacteria, diet and carcinogen exposure. Here, too, the ability to stave off the disease seems to depend on maintaining the appropriate microbial balance. Overweight mice and people have a different composition of gut microbiota from their lighter counterparts, and they have higher levels of DCA, too.

However, not everyone is convinced that individual bacterial species are to blame. Some researchers point out that dysbiosis, and therefore cancer risk, involves multiple strains of bacteria. And the bacterial mix can vary from person to person, meaning it is unlikely that scientists can pin all responsibility on a single species.

Others are looking for ways to promote the growth of healthy bacterial strains rather than target the bad ones....There is also some early clinical evidence that specially formulated probiotics — cocktails of good bacteria — can bump the microbiome back into balance. Hylemon and his colleagues gave people with cirrhosis a probiotic containing Lactobacillus bacteria and found that their blood markers of inflammation decreased along with their cognitive dysfunction (a common symptom of cirrhosis)6. Although the study was not designed to evaluate cancer risk, it does show that delivering bacteria to the gut can have positive therapeutic effects on the liver.